[English] 日本語
Yorodumi
- PDB-7xmv: E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A(AMP/A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xmv
TitleE.coli phosphoribosylpyrophosphate (PRPP) synthetase type A(AMP/ADP) filament bound with ADP, AMP and R5P
ComponentsRibose-phosphate pyrophosphokinase
KeywordsBIOSYNTHETIC PROTEIN / Allosteric enzyme / Kinase / Transferase / Nucleotide biosynthesis / ATP-binding / Magnesium / Manganese / Metal-binding / Nucleotide-binding
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / protein hexamerization / phosphate ion binding / ADP binding / kinase activity ...ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / protein hexamerization / phosphate ion binding / ADP binding / kinase activity / phosphorylation / magnesium ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / N-terminal domain of ribose phosphate pyrophosphokinase / Phosphoribosyl synthetase-associated domain / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / 5-O-phosphono-alpha-D-ribofuranose / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHu, H.H. / Lu, G.M. / Chang, C.C. / Liu, J.L.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)No. 2021YFA0804701-4 China
National Natural Science Foundation of China (NSFC)No. 31771490 China
CitationJournal: Elife / Year: 2022
Title: Filamentation modulates allosteric regulation of PRPS.
Authors: Huan-Huan Hu / Guang-Ming Lu / Chia-Chun Chang / Yilan Li / Jiale Zhong / Chen-Jun Guo / Xian Zhou / Boqi Yin / Tianyi Zhang / Ji-Long Liu /
Abstract: Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP ...Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP synthase (PRPS) is associated with human disorders, including Arts syndrome, retinal dystrophy, and gouty arthritis. Recent studies have demonstrated that PRPS can form filamentous cytoophidia in eukaryotes. Here, we show that PRPS forms cytoophidia in prokaryotes both in vitro and in vivo. Moreover, we solve two distinct filament structures of PRPS at near-atomic resolution using Cryo-EM. The formation of the two types of filaments is controlled by the binding of different ligands. One filament type is resistant to allosteric inhibition. The structural comparison reveals conformational changes of a regulatory flexible loop, which may regulate the binding of the allosteric inhibitor and the substrate ATP. A noncanonical allosteric AMP/ADP binding site is identified to stabilize the conformation of the regulatory flexible loop. Our findings not only explore a new mechanism of PRPS regulation with structural basis, but also propose an additional layer of cell metabolism through PRPS filamentation.
History
DepositionApr 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribose-phosphate pyrophosphokinase
E: Ribose-phosphate pyrophosphokinase
C: Ribose-phosphate pyrophosphokinase
D: Ribose-phosphate pyrophosphokinase
B: Ribose-phosphate pyrophosphokinase
F: Ribose-phosphate pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,82336
Polymers210,5056
Non-polymers6,31930
Water14,592810
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein / Sugars , 2 types, 12 molecules AECDBF

#1: Protein
Ribose-phosphate pyrophosphokinase / RPPK / 5-phospho-D-ribosyl alpha-1-diphosphate / Phosphoribosyl diphosphate synthase / ...RPPK / 5-phospho-D-ribosyl alpha-1-diphosphate / Phosphoribosyl diphosphate synthase / Phosphoribosyl pyrophosphate synthase / P-Rib-PP synthase / PRPP synthase / PRPPase


Mass: 35084.090 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: prs, prsA, b1207, JW1198
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A717, ribose-phosphate diphosphokinase
#2: Sugar
ChemComp-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 834 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: E.coli PRPP syhthetase filament structure complex with ADP,AMP, Mg2+ and R5P
Type: ORGANELLE OR CELLULAR COMPONENT / Details: a new allosteric for AMP binding / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The purifide monomer or oligomer protein was incubated with ADP,AMP and MgCl2 to form this type A(AMP/ADP) filament.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: blot for 3.5 seconds with blot force of -1 before plunge-freezing

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Image recordingAverage exposure time: 4 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2566

-
Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.1-betaparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7UCSF Chimera1.14model fitting
9Cootmodel refinement
10PHENIXmodel refinement
13RELION3.1-betaclassification
14RELION3.1-beta3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1066797
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53045 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4S2U

4s2u


Pdb chain-ID: A / Pdb chain residue range: 2-309
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00814598
ELECTRON MICROSCOPYf_angle_d0.76619854
ELECTRON MICROSCOPYf_dihedral_angle_d21.8522124
ELECTRON MICROSCOPYf_chiral_restr0.0512382
ELECTRON MICROSCOPYf_plane_restr0.0042550

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more